From my experience, the boat to and from MK is faster than the Monorail.
While anything can happen in terms of delays, I plan on (A) 30 minutes travel time for MK to and from Poly, (B) 45 minutes travel time for Epcot to and from Poly and © 1 hour travel time for HS or AK to and from Poly. Times might be less but that is what I would build into my schedule. Also, if I were trying to make an ADR, I would allow for a bit more travel time.
In terms of breaks with a 5 year old. If it were me, I would go back to the resort at lunch time for a long break on my MK days. For the days at the other parks, I would stay through the day and call it a night after dinner. Exception - with a 5 year old, I would plan 1 or 2 night events and on those days I would take a mid-day break no matter which park I was going to.